Cas9 nuclease is not one-size-fits-all. Determining the most appropriate Cas9 nuclease reagent for your experiment is dependent on the particular application or cell type. Take a look at the features in this table to get started on selecting the best product for you.
| ||Cas9 protein ||Cas9 mRNA ||Cas9 expression plasmid ||Lentiviral Cas9 plasmid ||Lentiviral Cas9 particles |
|DNA-free, transient |
|✔ ||✔ || || || |
|Co-electroporate with |
synthetic guide RNA
|✔ ||✔ || || || |
|Co-transfect with synthetic guide RNA ||✔ ||✔ ||✔ ||✔ || |
|Enrich population with |
| ||✔ ||✔ ||✔ ||✔ |
|Enrich population with |
| || ||✔ ||✔ ||✔ |
|Inducible expression || || || ||✔ ||✔ |
|Create stable cell lines || || || || ||✔ |
|Lentiviral transduction |
for cells that are difficult
| || || || ||✔ |
Gene editing with Edit-R Cas9 Nuclease mRNA and synthetic gRNA or crRNA and tracrRNA is performed by co-transfecting all components with DharmaFECT Duo Transfection Reagent (or other DharmaFECT transfection reagent suitable to your specific cells of interest). One may then observe phenotypes directly. A DNA mismatch detection assay can be used to estimate gene editing efficiency prior to clonal cell line generation and characterization.
A. Modifications to block degradation by nucleases are required for successful co-electroporation of Cas9 mRNA and crRNA:tracrRNA. B. Co-electroporation of Cas9 protein and crRNA:tracrRNA does not require stabilizing modifications, but results may be improved with their addition.
Edit-R Fluorescent Cas9 mRNA U2OS cells were plated at 10,000 cells/well in a black 96-well plate 24 hours before transfection. At the time of transfection, Edit-R™ EGFP Cas9 Nuclease mRNA (200 ng, Cat #CAS11860) or non-fluorescent Edit-R Cas9 Nuclease mRNA (200 ng, Cat #CAS11195) was co-transfected with Edit-R PPIB Synthetic crRNA Control (25 nM, Cat #U-007000-01-05) and tracrRNA (25 nM, Cat# U-002005-05) using DharmaFECT™ Duo transfection reagent (0.3 µL/well). After 24 hours, cells were imaged for EGFP fluorescence using the Nikon Eclipse Ti-S/L100 inverted microscope (A). At 72 hours after transfection, cells were harvested and gene editing was measured through a DNA mismatch detection assay (B).
U2OS cells expressing a Ubiquitin-tagged EGFP were plated at 10,000 cells/well in a black 96-well plate and co-transfected with Cas9 mRNA (200 ng, Cat #CAS11859) and synthetic tracrRNA (25 nM, Cat# U-002005-05) targeting PSMD11 (25 nM, Cat #CM-085161-03), a known proteasome component, or a Non-targeting control (NTC, Cat #U-007501-xx). Increasing amounts of DharmFECT Duo Transfection Reagent were tested per well (0.1 µL to 0.7 µL). After 24 hours, cells were imaged for mKate2 fluorescence using the In Cell Analyzer 2200. At 72 hours after transfection, cells were imaged for EGFP fluorescence resultant from proteasome knockout. Based on mKate2 fluorescence, optimal transfection conditions occur at 0.3-0.4 µL of DharmaFECT Duo per well which corresponds to an increased phenotypic effect. Above 0.4 µL of DharmaFECT Duo per well, significant cell death is observed (graph, red boxes). UT = untransfected sample.
U2OS cells were transfected with Edit-R mKate2-Cas9 mRNA (200 ng, Cat #CAS11859), EMX1-targeting crRNA (25 nM, Custom synthesis), tracrRNA (25 nM, Cat #U-002005) and a single-stranded donor oligo (5 nM, designed with the Edit-R HDR Donor Designer) to insert a NheI restriction site and a FLAG tag sequence at the C-terminus of EMX1. Transfections were done using DharmaFECT Duo transfection reagent (0.3 µL/well) 24 hours after plating 10,000 U2OS cells per well of a 96-well plate. Cells were then collected 24 hours after transfection and sorted into mKate2 fluorescent subpopulations (either Dim mKate2 fluorescence, Medium, or Top 10% fluorescence). Subpopulations were expanded for an additional 48 hours and analyzed for NheI insertion through Restriction Fragment Length Polymorphism (RFLP) by treating EMX1 PCR amplicons with NheI restriction enzyme.
HEK293T cells were plated in 6-well plates and transfected with hCMV-mKate2-Cas9 expression plasmid and crRNA:tracrRNA complex targeting the human PPIB gene in exon 2. Cells were harvested 72 hours post-transfection and sorted using the mKate2 fluorescent reporter. Fluorescent cells were plated at two, four or six individual cells per well in 96-well plates and further grown for clonal isolation. To precisely determine the genotype, Sanger sequencing was performed on PCR products amplified from gDNA spanning the crRNA target site and analyzed for indels. Various indels were observed, but notably, several of the clonal lines contained insertions homologous to components of the Cas9 expression plasmid. Similar observations were also reported in Hendel et al. (2014). See the Edit-R workflow Application Note for more experimental details.
HEK293T, A549 and U2OS cells were plated at 20,000 cells/well in 96-well plates and co-transfected using DharmFECT Duo Transfection Reagent with Cas9 mRNA (200 or 100 ng) and synthetic crRNA:tracrRNA (50 nM) targeting VEGFA. Cells were harvested 72 hours post-transfection and the relative frequency of gene editing was calculated based on a DNA mismatch detection assay with T7 Endonuclease I. The synthetic crRNA was designed using the Dharmacon CRISPR Design Tool. UT = untransfected sample.
HEK293T and U2OS cells were plated at 20,000 cells/well in 96-well plates and co-transfected using DharmFECT Duo Transfection Reagent with Cas9 mRNA (200, 100, 50, 25 or 10 ng) and synthetic crRNA:tracrRNA (50 nM) targeting VEGFA. Cells were harvested 72 hours post-transfection and the relative frequency of gene editing was calculated based on a DNA mismatch detection assay with T7 Endonuclease I. It is recommended to optimize the amount of Cas9 mRNA (50-200 ng/well in 96-well format) in your cells of interest and for your application. The synthetic crRNA targeting VEGFA was designed using the Dharmacon CRISPR Design Tool. UT = untransfected sample.